MEMP PhD Thesis Defense: Rohan Thakur

Droplet Microfluidic Technologies for Targeted Single Cell Sequencing

Droplet microfluidics has transformed how we study biology. By encapsulating biological samples in micron sized water-in-oil droplets, we can tailor the exact biochemical environment of each individual cell. When combined with DNA barcodes, this compartmentalization allows researchers to study genomes and transcriptomes at a single cell resolution at throughputs exceeding millions of cells per experiment. By integrating this single cell sequencing technology with additional microfluidic operations, we can perform targeted sequencing on ultra-rare cells of interest. We can recreate bulk assays in an miniaturized format and then physically enrich cell subtypes based on the results of that assay. These autonomous workflows are platform technologies but can be tailored for a specific biological application like the directed evolution of enzymes or the enrichment of rare viral sequences. In this dissertation, I present three projects that address key technology gaps in these workflows. Firstly, I present a novel method of picoinjection that can control the injected volume of each individual droplet. If the promise of droplet microfluidics is that we can create a micron-size test tube, picoinjection is the microfluidic analogy to the pipette we use to add and remove reagents. In our novel technique, we synchronize when we initiate picoinjeciton to allow an operator to tune the exact injected volume. Secondly, I present a low-cost imaging method that can resolve high speed droplet dynamics. By synchronizing the illumination with droplet dynamics, this imaging method can capture the precise time points required to tune high speed droplet operations like sorting and picoinjection. Finally, I demonstrate a novel method of targeted sequencing that integrates with live cell imaging. This method replaces the physical enrichment used in droplet sorting workflows with selective photocrosslinking. With this approach, we can isolate cells of interest according to a complex phenotype incompatible with enrichment schemes like droplet sorting or fluorescent activated cell sorting. Together, our work expands the toolkit available to perform targeted single cell genomics.

Thesis Supervisor:
David A. Weitz, PhD
Mallinckrodt Professor of Physics and Applied Physics, Harvard University
Director of the Materials Research Science and Engineering Center
Co-Director of the BASF Advanced Research Initiative
Member, Kavli Institute for Bionano Science & Technology

Thesis Committee Chair:
Mehmet Toner, PhD 
Helen Andrus Benedict Professor of Surgery and Bioengineering, Harvard Medical School & Massachusetts General Hospital
Professor, Harvard-MIT Division of Health Sciences and Technology 
Co-Director, Center for Engineering in Medicine & Surgery Director of Research, Shriners Hospitals for Children-Boston 

Thesis Reader:
Alex Shalek, PhD
Director, Institute for Medical Engineering and Science (IMES), MIT
Director, Health Innovation Hub
J.W. Kieckhefer Professor of Chemistry and IMES, MIT
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Rohan Thakur is inviting you to a scheduled Zoom meeting

Topic: Rohan Thakur MEMP PhD Thesis Defense
Time: Thursday, July 16, 2026, 9:00 AM Eastern Time (US and Canada)

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